Global Supercomputing Comes to Pittsburgh

From November 6-12 more than 6,000 people from around the world will
gather at Pittsburgh’s David Lawrence Convention
Center for SC2004. The annual
conference of the global supercomputing community brings together
equipment and software manufacturers, researchers and others to share
ideas and assess new developments in high-performance computing,
networking and storage.

Through the efforts of PSC executive director Beverly Clayton, who serves on
the steering committee, and other PSC staff, the conference is in Pittsburgh
for the second time — having been here before in 1996 — with an
associated economic boon estimated at $9 million.

Economic Development

Teacher Tech ‘04

Pittsburgh-area science teachers are using a Calculator Based
Laboratory, a hand-held, data-collection system that works with
various sensor technologies.
From August 2-6, PSC sponsored a weeklong workshop for
Pittsburgh-area science teachers. Presented in collaboration
with Rice University’s Center for Equity and Excellence
in Education and the National Science Foundation, the workshop
introduced new technologies for helping to teach science and
raised awareness about teacher roles in shaping and encouraging
the next generation of scientists.

PSC’s high-performance computing and networking help to boost the
competitiveness of Pennsylvania business and industry and are among the
resources the state can point to in attracting new business. Recognizing this,
the Pennsylvania Department of Economic and Community Development features PSC
machine time and consulting in incentive packages it offers to select
companies.

As a PSC Industrial Affiliate, Pittsburgh-based PPG Industries uses
LeMieux, PSC’s terascale system, and the quantum-chemistry
program
GAUSSIAN for computational modeling in several aspects of its
product lines as a global supplier of coatings, glass, fiberglass and
chemicals.

This year PSC presented a third annual customized technology-briefing day to
staff from the Bechtel Bettis Atomic Power Laboratory in Pittsburgh. PSC
consultants provided information on how to develop, manage and use a parallel
distributed-computing environment.

Research in Pennsylvania

Ken Merz, Pennsylvania State University.

By supporting Pennsylvania university researchers, PSC resources help to
attract research funds to the state. During the past year, more than 290
Pennsylvania researchers from 11 institutions used PSC computing. Pennsylvania
usage of PSC’s CRAY T3E totaled 1.25 million hours. In addition,
Pennsylvania researchers received allocations through NSF of nearly 10 million
hours on LeMieux, PSC’s terascale system, along with 450,000 hours on
PSC’s HP Marvel systems. The projects represented here (facing page)
exemplify how supercomputing plays a role in scientific and engineering
research in Pennsylvania.

Biomolecules and the Search for Drugs

Using LeMieux, PSC’s terascale system, Merz carried out a
quantum-mechanical study of urease, a metalloenzyme that plays
important roles in the nitrogen metabolism of plants and
microbes. Urease in soil can release large quantities of toxic
ammonia, affecting crop yields, and it also constitutes a
virulence factor in human and animal infections of the urinary
tract. This graphic from PSC calculations shows details of the
urease active-site structure.

Professor Ken Merz of Penn State’s Department of
Chemistry leads a research group that develops and uses computational
methods to further understanding of biomolecules. They are especially
interested in metalloenzymes, an important class of enzymes that carry
out myriad biological functions. These enzymes are involved in diseases
ranging from periodontal disease to arthritis and cancer, and drugs
that inhibit and regulate these enzymes could be useful in treating
these diseases.

Merz, who is also CEO of QuantumBio Inc, a
biotechnology company he cofounded, works on developing improved
computational techniques that include quantum-mechanical approaches
— highly precise and at the same time computationally expensive
— together with more conventional classical approaches. Some of
his recent work has focused on an approach that will make it feasible
to carry out fully quantum calculations on molecules as large as
enzymes.

When the Earth Shakes

One of the main lessons of recent urban earthquakes is the need for better
information about where and how much the ground will shake. A
multi-disciplinary team led by Jacobo Bielak, Omar Ghattas and David
O’Hallaron of Carnegie Mellon University have used LeMieux, PSC’s
terascale system, to simulate soil conditions for the Los Angeles earthquake
basin with much greater accuracy than has before been possible.
For this work, they received the 2003 Gordon Bell Prize, one of high-performance
computing’s most prestigious awards, and their work was recognized as a
finalist for the 2004 Computerworld award in Science.

Using 3,000 LeMieux processors, they carried out the most detailed simulation
yet of the 1994 Northridge earthquake, allowing soil to vibrate at two cycles
per second, doubling the previous high frequency for earthquake simulation.
Because of LeMieux, this group also made significant progress on the
“inverse problem,” a sophisticated approach that makes it possible
to recover deep geological features based on seismic recordings at the surface.